Same situation in Dol now. White towers from nature stopped appearing. This happened after about 10 waves and after the transmutation of white cards of nature and after the build of beavers and dandelion
I’ll get better a little. In DoL, the blue towers of nature also ceased to appear, although the game warns of their appearance. Moreover, only wolves appear, without warning. Periodically transmuting any items does not give a better item.
It's likely the new transmute system. I think that will change in 2.1, but right now it's at a weird spot.
If you check the double tap transmute many, you'll see that it now says "and all future drops."
If you want to stop transmuting, then go to the game menu (the (1) button), then long press on the type of card you want to stop transmuting (towers in this case), then you can swipe through the towers and select "stop transmuting" on the card you'd like to see again.